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1 <tool id="cfsan_snp_pipeline_merge_sites" name="CFSAN SNP Pipeline: merge sites" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>from multiple samples</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 python '$__tool_directory__/snp_wind.py' ./
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9 #if str($input_type_cond.input_type) == 'single':
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10 -n '$input_vcf.element_identifier'
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11 -f '$input_vcf'
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12 #else:
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13 #for $input_vcf in $input_vcf_collection
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14 -n '$input_vcf.element_identifier'
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15 -f '$input_vcf'
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16 #end for
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17 #end if
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18 -p 'var.fit.vcf' > ./file
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19 && cfsan_snp_pipeline merge_sites -v 4 -n 'var.fit.vcf' ./file ./filtered_snps -o '$output'
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20 ]]></command>
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21 <inputs>
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22 <expand macro="input_type_cond"/>
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23 </inputs>
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24 <outputs>
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25 <data name="output" format="tabular"/>
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26 </outputs>
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27 <tests>
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28 <test>
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29 <param name="input_type" value="collection"/>
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30 <param name="input_vcf_collection">
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31 <collection type="list">
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32 <element name="input1" value="input1.vcf" ftype="vcf"/>
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33 <element name="input2" value="input2.vcf" ftype="vcf"/>
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34 <element name="input3" value="input3.vcf" ftype="vcf"/>
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35 <element name="input4" value="input4.vcf" ftype="vcf"/>
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36 </collection>
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37 </param>
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38 <output name="output" value="output.tabular"/>
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39 </test>
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40 </tests>
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41 <help><![CDATA[
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42 **What it does**
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43
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44 Combine the SNP positions across all samples into a single unified SNP list
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45 file identifing the positions and sample names where SNPs were called.
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46
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47 **Optional parameters**
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48
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49 * **force** - Force processing even when result file already exists and is newer than inputs (default: False)
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50 * **vcfname** - File name of the VCF files which must exist in each of the sample directories (default: var.flt.vcf)
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51 * **maxsnps** - Exclude samples having more than this maximum allowed number of SNPs. Set to -1 to disable this function (default: -1)
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52
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53 **More information**
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54
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55 CFSAN SNP Pipeline `merge sites documentation <https://snp-pipeline.readthedocs.io/en/latest/cmd_ref.html#merge-sites>`_
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56 ]]></help>
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57 <expand macro="citations"/>
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58 </tool>
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59
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